Methods and reagents for maintaining the viability of cancer cells in surgically removed tissue

ABSTRACT

A composition and method for generating reagents and the composition of these reagents for the stabilization and preservation of viability of cancer tissue which has been surgically excised and the suspension and/or termination of apoptosis (cell death) by significant modulation of cell metabolism by low molar concentrations of synergistic chemistries and hormonal growth enhancers while maintaining normal gene expression patterns of the surgically excised tissue.

CROSS REFERENCE

The present patent application is a continuation application ofnonprovisional patent application Ser. No. 14/211,578 filed on Mar. 14,2014, which claims the benefit of provisional patent application61/798,627 filed on Mar. 15, 2013, both of which are herein incorporatedby reference.

FIELD

This invention pertains to methods of generating reagents and thecomposition of reagents for the stabilization, preservation, andviability of cancer tissue which has been surgically excised.

BACKGROUND

Surgical tissue collection for pathology analysis to detect cancer cellsfrom excised tissue has been the standard practice in cancer diagnosisfor decades. The current protocols for tissue sample collection call forexcised tissue to be collected and placed in a formalin solution, andthen transported to the pathology laboratory for staining and analysis.Unfortunately, formalin fixes cells (e.g. kills the cells) and in theprocess causes significant changes in the cellular integrity whichproduces problems with the ability to accurately conduct genomic testing(RNA, mRNA and protein biomarker analysis, and gene expression studies)analyses.

Molecular technology, such as genomic testing with real-time polymerasechain reaction technology (qPCR), has evolved to the extent that certaincancers can be matched to specific chemotherapies that have been shownto respond to certain gene expression patterns found in the cancercells. Thus, being able to obtain accurate gene expression patterns ofthe cancer cells excised from a patient allows for personalizedhealthcare by designing individualized chemotherapy as well as othertreatments. This is a very important shift in treatment paradigms andwill represent the standard of care in the near future.

Cancer tissue samples which have been preserved in formalin are notviable tissue samples for completing gene expression analyses. Onereason formalin is not a good reagent for achieving gene expressionanalysis on tissue samples is that formalin causes the slow crosslinking of proteins into a mesh network, and valuable target proteinsmay be destroyed by the formalin process as they are not protected fromdegradation.

Furthermore, as formalin penetrates the tissue sample, cell death(apoptosis) occurs. Cancer cells are unique as they have a metabolicpre-programmed apoptosis, thus accelerated apoptosis occurs in formalin.As the cells in the tissue sample die, a subset of the total cellpopulation lyse and release a broad range of internal regulatory enzymeswhich further cause accelerated cell death. A number of these enzymeswill degrade or destroy target nucleic acids, DNA, RNA, mRNA, regulatoryproteins, and associated biomarkers used in molecular genomic analysis.During the fixation process, while the formalin kills the cells in thetissue sample, gene expression can become erratic and genomic expressionof critical genes can become under expressed or over expressed, givinginaccurate values of the expression of certain cancer genes. This is amajor problem when chemotherapy decisions are based on the levels ofspecific mRNA from selected genes. Thus, accurate genomic testing ofcancer cells fixed in formalin is not possible at present.

It should also be noted that fixing the proteins and cells in a tissuesample with formalin takes about 48 hours to occur. Making the formalinprocess not very exact at determining what the genetic expression is atthe time of tissue collection from a patient.

In general, the scientific usefulness of genetic data obtained fromtissue fixation is directly related to the quality of the tissue and theusefulness of that tissue for genomic testing. Presently, formalinfixation is not very useful in obtaining accurate genetic expressioninformation. Thus there is a need for reagents for fixing tissuesamples, so that the collected sample comprises accurate gene expressionmarkers for genetic testing.

There is also a need for tissue sample fixation reagents that are not ashazardous as formalin. Unfortunately, formalin carries a significantrisk of cancer to the users, as well as significant state and federalregulations for the use and disposal of the products containingformalin.

The present invention discloses methods for manufacturing reagents andthe composition of reagents which allow for the collection of cancertissue surgically removed from a patient, in which the genetic cellularinformation of the cancer cells in the tissue sample are maintained in aviable state, making the tissue sample suitable for genetic expressionanalysis.

SUMMARY

The present invention discloses novel methods to produce a cellviability reagent for tissue samples such as biopsy samples, whichallows for genetic expression analysis of the cells in the sample.

In most embodiments of the methods of producing a reagent for tissuesamples, the method comprises providing at least one chaotrope,providing at least one kosmotrope, providing a chelator, providing abuffer, providing an apoptosis substrate, providing a metabolicmodulator, and mixing the chaotrope, kosmotrope, chelator, buffer,apoptosis substrate, and the metabolic modulator in such a manner as toenable the gene expression analysis of the tissue sample.

In many embodiments of the methods for producing the reagent for tissuesamples, the apoptosis substrate is a cancer cell apoptosis substrateand the tissue sample is a surgically excised cancer tissue.

In most embodiments of the methods of the invention, the finalconcentration of the chaotrope is from about 0.1 molar (0.1 M) to about2 M, the kosmotrope is from about 0.1 M to about 2 M, the chelator isfrom about 0.1 M to about 2 M, and the apoptosis substrate is from about0.001 M to about 0.5 M in the reagent for tissue samples.

In certain embodiments of the methods of the invention, the chaotrope isselected from the group consisting of SCN (sodium thiocyanate), H₂PO₄ ⁻,HCO₃ ⁻, I⁻, Cl⁻, NO₃ ⁻, NH₄ ⁺, Cs⁺, K⁺, (NH₂)₃C⁺, guanidinium, all saltsof guanidinium, Br⁻, or Rb⁺.

In some embodiments of the method of making the reagent, the at leastone kosmotrope is selected from the group consisting of Glycerol,Trimethylamine N-oxide, Ectoine, α,α-Trehalose,3-Dimethylsulfoniopropionate, Glucose, Dextran, or D-Lactose.

In other embodiments the chelator is selected from the group consistingof EDTA, EGTA, or BAPTA.

In another embodiment of the methods of the invention, the buffer isselected from the group consisting of BIS-TRIS, BIS-TRIS Propane, HEPES,HEPES Sodium Salt, MES, MES Sodium salt, MOPS, MOPS sodium salt, sodiumsalt or sodium phosphate buffer (monobasic, tribasic PO₄).

In yet another embodiment of the method, the apoptosis substrate isselected from the group consisting of DMSO, Leptin, Glycine betaine,potassium citrate, Trimethylamine, proline, NDSB 195, L-Arginine,Xylitol, Sodium selenite, NDSB 201, CuCl₂, or CTAB.

In some embodiments the metabolic modulator is selected from the groupconsisting of polar aprotic solvents, DMSO, Acetone,N,N-Dimethylformamide, or Acetonitrile.

In most embodiments, the methods of producing the reagent furthercomprise adding the various components of the reagent to an aliquot ofpurified water in the sequential order of adding at least one chaotrope,followed by the addition of the chelator, followed by the addition ofthe metabolic modulator, followed by the addition of a first kosmotrope,followed by the addition of the buffer, followed by the addition of asecond kosmotrope which is different from the first kosmotrope, andfinally followed by the addition of the apoptosis substrate.

In many embodiments of the invention the chaotrope is SCN⁻ (sodiumthiocyanate), the first kosmotrope is glycerol and the second kosmotropeis α,α-Trehalose, the chelator is EDTA, the buffer is Sodium PhosphateBuffer (monobasic, tribasic PO₄), the cell apoptosis substrate isleptin, and the metabolic modulator is DMSO.

In another embodiment the method of manufacturing a reagent foranalyzing tissue samples comprises providing an aliquot of purifiedwater, adding components of the reagent to the purified water in thefollowing order: adding sodium thiocyanate, EDTA, DMSO, glycerol,potassium phosphate buffer, and α,α-Trehalose, followed by adding humanleptin and mixing the components between each addition of the variouscomponents in a manner that allows for accurate genetic expressionanalysis of the tissue sample or biopsy.

In some embodiments the method of manufacturing a reagent for analyzingtissue samples comprises providing an aliquot of purified water, addingcomponents of the reagent to the purified water in the following order:adding at least one chaotrope, followed by the addition of a chelator,followed by the addition of a metabolic modulator, then adding a firstkosmotrope, then adding a buffer, followed by adding a second anddifferent kosmotrope, followed by adding an apoptosis substrate, andmixing the components between each addition of components in a mannerthat allows for accurate genetic expression analysis of the tissuesample.

In most embodiments the reagent for preparing tissue samples whichallows for genetic expression analysis comprises at least one chaotrope,at least one kosmotrope, a chelator, a buffer, an apoptosis substrate,and a metabolic modulator.

For analyzing cancer tissue samples, the apoptosis substrate is a cancercell apoptosis substrate.

For most embodiments of the reagent, the final concentration for thechaotrope is from about 0.1 M to about 2 M, the at least two kosmotropesare from about 0.1 M to about 2 M for each kosmotrope, the chelator isfrom about 0.1 M to about 2 M, and the apoptosis substrate is from about0.001 M to about 0.5 M.

In specific embodiments of the reagent, the chaotrope is SCN⁻ (sodiumthiocyanate), the kosmotropes are glycerol and α,α-Trehalose, thechelator is EDTA, the buffer is Sodium Phosphate Buffer (monobasic,tribasic PO₄), the cell apoptosis substrate is leptin, and the metabolicmodulator is DMSO.

In some embodiments of the reagent the chaotrope is selected from thegroup consisting of SCN (sodium thiocyanate), H₂PO₄ ⁻, HCO₃ ⁻, I⁻, Cl⁻,NO₃ ⁻, NH₄ ⁺, Cs⁺, K⁺, (NH₂)₃C⁺, guanidinium, all salts of guanidinium,Br⁻, or Rb⁺.

In yet other embodiments of the reagent, the kosmotrope is selected fromthe group consisting of Glycerol, Trimethylamine N-oxide, Ectoine,α,α-Trehalose, 3-Dimethylsulfoniopropionate, Glucose, Dextran, orD-Lactose.

In yet another embodiment of the reagent the chelator is selected fromthe group consisting of EDTA, EGTA, or BAPTA.

The preserving reagent in some embodiments comprises a buffer which isselected from the group consisting of BIS-TRIS, BIS-TRIS Propane, HEPES,HEPES Sodium Salt, MES, MES Sodium salt, MOPS, MOPS Sodium Salt, Sodiumsalt or Sodium Phosphate Buffer (monobasic, tribasic PO₄).

In other embodiments of the reagent, the apoptosis substrate is selectedfrom the group consisting of DMSO, Leptin, Glycine betaine, potassiumcitrate, Trimethylamine, proline, NDSB 195, L-Arginine, Xylitol, Sodiumselenite, NDSB 201, CuCl₂, or CTAB.

While yet another embodiment of the reagent comprises the metabolicmodulator being selected from the group consisting of polar aproticsolvents, DMSO, Acetone, N,N-Dimethylformamide, or Acetonitrile.

All patents and publications identified herein are incorporated byreference in their entirety.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a flow chart showing one embodiment of the method of producinga reagent for surgically removed tissue, which allows for geneticexpression analysis of the tissue sample in accordance with theinvention.

FIG. 2 is a flow chart showing one embodiment of the method ofmanufacturing a reagent for surgically removed tissue, particularlycancerous tissue, which allows for genetic expression analysis of thetissue sample in accordance with the invention.

FIGS. 3A and 3B are a formulation sheet showing one embodiment of thecomponents of a reagent used for preserving tissue samples and thesequential addition of each component in accordance with the invention.

FIG. 4 is a graph of reverse transcriptase RT-PCR results of the PGKgene from aged LNCaP-FGC cells, comparing the use of one embodiment ofthe cell preserving reagent in accordance with the invention toconventional preserving reagents.

FIG. 5 is a graph of mRNA copies of the PBGD gene from aged PC3 cancercells, comparing reverse transcriptase RT-PCR results of one embodimentof the cell preserving reagent in accordance with the invention toconventional reagents.

FIG. 6 is a graph of mRNA copies of G6PDH of various aged renal cancercells, comparing the use of one embodiment of the preserving reagent toconventional preserving solutions.

FIG. 7 is a graph comparing three different embodiments of thepreserving reagent used on aged renal cancer cells.

DESCRIPTION

Unless otherwise stated, the following terms used in this application,including the specification and claims, have the definitions givenbelow. It must be noted that as used in the specification and theappended claims, the singular forms “a,” “an,” and “the” include pluralreferents unless the context clearly dictates otherwise.

“Optional” or “optionally” means that the subsequently described eventor circumstance may but need not occur, and that the descriptionincludes instances where the event or circumstance occurs and instancesin which it does not.

The terms “those defined above” and “those defined herein” whenreferring to a variable incorporates by reference the broad definitionof the variable as well as preferred, more preferred, and most preferreddefinitions, if any.

The term chaotrope refers to compounds that interact weakly with watermolecules and disrupt the water molecule hydrogen bonded network aroundprotein molecules.

The term kosmotrope refers to compounds that interact strongly withwater molecules, and organize water molecules in a typically favorablemanner around protein molecules. A biomaterial stabilizing compositionmay include a kosmotrope in some embodiments. Without being limited toany specific mechanism(s) of action, a kosmotrope, in some embodiments,may stabilize and/or improve water-water interactions in an aqueouscomposition. Examples of kosmotropes may include, without limitation,glycerol, proline (e.g., L-proline), trehalose (e.g., D-(+) trehalose,D-(+) trehalose dihydrate), α,α-Trehalose, glycine betaine, glucose,dextrose, glutamic acid, and/or aspartic acid. Examples of a kosmotrope,in some embodiments, may include SO₄ ⁻, HPO₄ ⁻, Ca²⁺, Mg²⁺, Li⁺, Na⁺,OH⁻, and/or PO₄ ²⁻.

The term buffer refers to compound which gives a mixture a pH from about4.5 to about 8.5. In some embodiments, a suitable buffer may be selectedfrom Good buffers (e.g., HEPES), potassium acetate, sodium phosphate,potassium bicarbonate, tris(hydroxyamino)methane (Tris), andcombinations thereof. For example, a buffer may include potassiumacetate, sodium acetate, potassium phosphate (mono, tribasic), sodiumphosphate, Tris, N-(2-hydroxyethyl)piperazine-N′-(2-ethanesulfonic acid)(HEPES) buffer, 3-(N-morpholino)propane sulfonic acid (MOPS) buffer,2-[(2-amino-2-oxoethyl)amino]ethanesulfonic acid (ACES) buffer,N-(2-acetamido)-2-iminodiacetic acid buffer (ADA),3-[(1,1-dimethyl-2-hydroxyethyl)amino]-2-propanesulfonic acid (AMPSO)buffer, N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid (BES) buffer,Bicine (N,N-bis(2-hydroxyethylglycine) buffer,bis-(2-hydroxyethyl)imino-tris(hydroxymethyl)methane (Bis-Tris) buffer,3-(cyclohexylamino)-1-propanesulfonic acid (CAPS) buffer,3-(cyclohexylamino)-2-hydroxy-1-propanesulfonic acid (CAPSO) buffer,2-(N-cyclohexylamino)ethanesulfonic acid (CHES) buffer,3-[N,N-bis(2-hydroxyethyl)amino]-2-hydroxy-propanesulfonic acid (DIPSO)buffer, N-(2-hydroxyethylpiperazine)-N′-(3-propanesulfonic acid) (HEPPS)buffer, N-(2-hydroxyethyl)piperazine-N′-(2-hydroxypropancsulfonic acid)(HEPPSO) buffer, 2-(N-morpholine)ethanesulfonic acid (MES) buffer,triethanolamine buffer, imidazole buffer, glycine buffer, ethanolaminebuffer, phosphate buffer, 3-(N-morpholine)-2-hydroxypropanesulfonic acid(MOPSO) buffer, piperazine-N,N′-bis(2-ethanesulfonic acid) (PIPES)buffer, piperazine-N,N′-bis(2-hydroxypropanesulfonic acid) (POPSO)buffer, N-tris[(hydroxymethyl)methyl]-3-aminopropanesulfonic acid (TAPS)buffer, 2-hydroxy-3-[tris(hydroxymethyl)methylamino]-1-propanesulfonicacid (TAPSO) buffer, N-[Tris(hydroxymethyl)methyl]-2-aminoethanesulfonicacid (TES) buffer, N-[Tris(hydroxymethyl)methyl]glycine (tricine)buffer, 2-amino-2-methyl-1,3-propanediol buffer,2-amino-2-methyl-1-propanol buffer, and combinations thereof.

The term chelator refers to a compound that may bind available metals(e.g., Mg²⁺ and Ca²⁺) to such an extent that metals that remainavailable to the metal-dependent enzymes (e.g., deoxyribonucleases) areinsufficient to support catalysis (i.e., nucleic acid degradation). Forexample, a metal independent enzyme may include a DNA ligase (e.g., D4DNA ligase), a DNA polymerase (e.g., T7 DNA polymerase), an exonuclease(e.g., exonuclease 2, lamda-exonuclease), a kinase (e.g., T4polynucleotide kinase), a phosphotase (e.g., BAP and CIP phosphotase), anuclease (e.g., BL31 nuclease and XO nuclease), and an RNA-modifyingenzyme (e.g., RNA polymerase, SP6, T7, T3 RNA polymerase, and T4 RNAligase).

A chelator may include, for example, ethylenediaminetetraacetic acid(EDTA), [ethylenebis(oxyethylenenitrilo)]tetraacetic acid (EGTA) and1,2-bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid (BAPTA), and/orsalts thereof. A chelator may be present at any desirable concentration.Where two or more chelators are included in a single reagent, either theconcentration of each chelator or the total concentration of thecombined chelators may fall within any of the provided ranges. In someembodiments, a chelator may include EDTA, EGTA, BAPTA, imidazole,iminodiacetate (IDA), bis(5-amidino-2-benzimidazolyl)methane (BABIM),and/or salts thereof.

The term metabolic modulator refers to penetrants/metabolic modulatorsthat act to optimize membrane penetration of chemistries within thereagent formulation, as well as stabilizing gene expression of cells,and in particular, hypoxic cancer cells.

The term apoptosis is the process of programmed cell death (PCD) thatmay occur in multicellular organisms. Biochemical events lead tocharacteristic cell changes (morphology) and death. These changesinclude blebbing, cell shrinkage, nuclear fragmentation, chromatincondensation, and chromosomal DNA fragmentation. (See also apoptotic DNAfragmentation).

The term “apoptosis substrate” is a compound or molecule which is a keycomponent in the reduction of apoptosis. An apoptosis substrate workssynergistically with other reagent formulation components to preventapoptosis and foster cell stability and cell growth.

The term “genetic expression analysis” refers to analyses that deal withdetecting the over expression, under expression or differentiallyexpressed genes of a cell, particularly in cancer cells.

The terms “overexpress,” “overexpression,” or “overexpressed”interchangeably refer to a protein or nucleic acid (RNA) that istranslated or transcribed at a detectably greater level, usually in acancer cell, in comparison to a normal cell. The term includesoverexpression due to transcription, post transcriptional processing,translation, post-translational processing, cellular localization (e.g.,organelle, cytoplasm, nucleus, cell surface), and RNA and proteinstability, as compared to a normal cell. Overexpression can be detectedusing conventional techniques for detecting mRNA (i.e., RT-PCR (reversetranscriptase-PCR), PCR, hybridization) or proteins (i.e., ELISA,immunohistochemical techniques). Overexpression can be 10%, 20%, 30%,40%, 50%, 60%, 70%, 80%, 90% or more in comparison to a normal cell. Incertain instances, overexpression is 1-fold, 2-fold, 3-fold, 4-fold, orhigher levels of transcription or translation in comparison to a normalcell.

The terms “underexpress,” “underexpression,” or “underexpressed” or“downregulated” interchangeably refer to a protein or nucleic acid thatis translated or transcribed at a detectably lower level in a cancercell, in comparison to a normal cell. The term includes underexpressiondue to transcription, post transcriptional processing, translation,post-translational processing, cellular localization (e.g., organelle,cytoplasm, nucleus, cell surface), and RNA and protein stability, ascompared to a control. Underexpression can be detected usingconventional techniques for detecting mRNA (i.e., RT-PCR, PCR,hybridization) or proteins (i.e., ELISA, immunohistochemicaltechniques). Underexpression can be 10%, 20%, 30%, 40%, 50%, 60%, 70%,80%, 90% or less in comparison to a control. In certain instances,underexpression is 1-fold, 2-fold, 3-fold, 4-fold, or lower levels oftranscription or translation in comparison to a control.

The term “differentially expressed” or “differentially regulated” refersgenerally to a protein or nucleic acid that is overexpressed(upregulated) or underexpressed (downregulated) in one sample comparedto at least one other sample, generally in a cancer patient compared toa sample of non-cancerous tissue in the context of the presentinvention.

The term “tumor” as used herein refers to all neoplastic cell growth andproliferation, whether malignant or benign, and all pre-cancerous andcancerous cells and tissues.

The terms “cancer” and “cancerous” refer to or describe thephysiological condition in mammals that is typically characterized byunregulated cell growth. Examples of cancer include, but are not limitedto, breast cancer, ovarian cancer, colon cancer, lung cancer, prostatecancer, hepatocellular cancer, gastric cancer, pancreatic cancer,cervical cancer, liver cancer, bladder cancer, cancer of the urinarytract, thyroid cancer, renal cancer, carcinoma, melanoma, and braincancer.

Biological or tissue sample includes sections of tissues such as biopsyand autopsy samples. A biological sample is typically obtained from aeukaryotic organism, most preferably a mammal such as a primate (e.g.,chimpanzee or human), cow, dog, cat, a rodent (e.g., guinea pig, rat, ormouse), rabbit, or a bird, reptile, or fish.

A biopsy refers to the process of removing a tissue sample fordiagnostic or prognostic evaluation, and to the tissue specimen itself.Any biopsy technique known in the art can be applied to the diagnosticand prognostic methods of the present invention. The biopsy techniqueapplied will depend on the tissue type to be evaluated (e.g., lungetc.), the size and type of the tumor, among other factors.Representative biopsy techniques include, but are not limited to,excisional biopsy, incisional biopsy, needle biopsy, surgical biopsy,and bone marrow biopsy. An excisional biopsy refers to the removal of anentire tumor mass with a small margin of normal tissue surrounding it.An incisional biopsy refers to the removal of a wedge of tissue fromwithin the tumor. A diagnosis or prognosis made by endoscopy orradiographic guidance can require a “core-needle biopsy” or a“fine-needle aspiration biopsy” which generally obtains a suspension ofcells from within a target tissue.

Therapeutic treatment and cancer therapies refer to chemotherapy,hormonal therapy, radiotherapy, immunotherapy, and biologic (targeted)therapy.

The term PCR refers to polymerase chain reaction. This refers to anytechnology where a nucleotide is amplified via temperature cyclingtechniques in the presence of a nucleotide polymerase, preferably a DNApolymerase. This includes but is not limited to real-time PCR (qPCR)technology, reverse transcriptase PCR (RT-PCR), and standard PCRmethods.

The present invention discloses methods for manufacturing a reagent formaintaining cellular viability of tissue samples which enables theanalysis of genetic expression of the cells in the tissue sample. Thepresent invention also relates to reagent compositions which allow forthe testing of accurate gene expression of viable cells in tissuesamples, particularly cancer cells. The methods for making the cellviability reagent, in general, have a sequential addition ofcompounds/molecules to achieve the optimum formulation of the reagent ofthe invention.

Referring to FIG. 1, there is a flow chart of one embodiment of themethods of manufacturing a cell viability reagent in accordance with theinvention. The method 100 for generating a cell viability reagentcomprises providing a chaotrope at event 110. The chaotrope is added toan aliquot of purified water. The chaotrope is a molecule which hasactivity against enzymes that degrade nucleic acids such as DNAases andRNAases, proteases, and regulatory enzymes responsible for proteindestruction and apoptosis. A chaotrope also has significant effects onwater distribution in cells and associated metabolic attenuation.

In most embodiments, the chaotrope is at least one of the followingcompounds; SCN(sodium thiocyanate), H₂PO₄ ⁻, HCO₃ ⁻, I⁻, Cl⁻, NO₃ ⁻, NH₄⁺, Cs⁺, K⁺, (NH₂)₃C⁺, guanidinium, all salts of guanidinium, Br⁻, orRb⁺. All of these compounds are known to have effects on waterdistribution around a cell and help in maintaining cell viability.

In some embodiments, the chaotrope has a final concentration in the cellviability reagent of concentrations ranging from about 0.1 M to about 2M, more preferably from at least about 1 mM, at least about 10 mM, atleast 0.05 M, at least about 0.1 M at least 0.5 M at least about 1 M, atleast about 1.75 M, at least about 2 M, to a maximum of at least about 3M.

At event 120, method 100 comprises providing at least one chelator. Thechelator is added to the cell viability formulation to help in theinactivation of Ca²⁺, Mg²⁺, driven enzyme systems that degrade nucleicacids. In this embodiment, the chelator is selected from the followinggroup of compounds: EDTA, EGTA, or BAPTA.

In most embodiments of the method of formulating the cell viabilityreagent, the chelator is found at a final concentration of about 0.1 Mto about 2 M, more preferably from about at least about 0.1 M, at leastabout 0.005 M, at least about 0.01 M, at least about 0.05 M, and/or atleast about 0.1 M.

At event 130, the method 100 further comprises providing a metabolicmodulator/penetrant compound. The metabolic modulator acts to optimizemembrane penetration of chemistries as well as acting as a carrier forlarge molecules such as glycerol. Additionally, it acts as a profoundmodulator of cell differentiation and function. The metabolic modulatoris a key component in stabilizing gene expression of hypoxic cancercells.

In the method 100, the metabolic modulator/penetrant is selected fromthe group consisting of polar aprotic solvents, DMSO, Acetone,N,N-Dimethylformamide, or Acetonitrile. The final concentration of themetabolic modulator in the formulations is from at least 0.25 M, atleast about 0.5 M, at least about 0.75 M. at least about 1 M, at leastabout 1.5 M, to a maximum of about 2 M.

The method 100 further comprises providing at least one kosmotrope formanufacturing the cell viability reagent at event 140. In thisembodiment the kosmotrope(s) is added to the mixture after the additionof the chaotrope. The kosmotrope(s) maybe one of the followingcompounds: Glycerol, Trimethylamine N-oxide, Ectoine, α,α-Trehalose,3-Dimethylsulfoniopropionate, Glucose, Dextran or D-Lactose. Thekosmotrope(s) has protective effects for nucleic acids, proteins andprotein folding, and is a necessary component of the reagent thatsynergizes with chaotropes for cell and membrane stability and metabolicmodulation for stabilization of gene expression when cells are stressed.

In some embodiments that kosmotrope is found in a final concentration ofthe cell viability reagent in concentrations ranging from about 0.1 M toabout 2 M, or from about 0.1 mM to about 100 mM, from about 1 mM toabout 10 mM, from about 0.1 M about 1.0 M to about 2.0 M, from about 0.1M to about 5.0 M.

At event 150, method 100 comprises providing for at least one bufferwhich is added to the formulation to adjust the pH of the cell viabilityreagent. The buffer in most embodiments is selected from the groupconsisting of BIS-TRIS, BIS-TRIS Propane, HEPES, HEPES sodium salt, MES,MES sodium salt, MOPS, MOPS Sodium Salt, Sodium salt or Sodium PhosphateBuffer (monobasic, tribasic PO₄).

In most embodiments, the final pH of the cell viability reagent is fromabout 4.5 to about 8, more preferably from about 5.0 to about 5.5 toabout 5.5 to 6.0, to about 6.5, to about 7.0 to about 7.5.

The method 100 further comprises providing a second kosmotrope formanufacturing the cell viability reagent at event 160. In thisembodiment the kosmotrope(s) is added to the mixture after the additionof the buffer. The kosmotrope(s) maybe one of the following compounds:Glycerol, Trimethylamine N-oxide, Ectoine, α,α-Trehalose,3-Dimethylsulfoniopropionate, Glucose, Dextran, or D-Lactose. Thekosmotrope(s) has protective effects for nucleic acids, proteins andprotein folding, and is a necessary component of the reagent thatsynergizes with chaotropes for cell and membrane stability and metabolicmodulation for stabilization of gene expression when cells are stressed.

In some embodiments that kosmotrope is found in a final concentration ofthe cell viability reagent in concentrations ranging from about 0.1 M toabout 2 M, more preferably from about 0.1 mM to about 100 mM, from about1 mM to about 10 mM, from about 0.1 M about 1.0 M to about 2.0 M, fromabout 0.1 M to about 5.0 M.

The method 100 further comprises providing an apoptosis substrate atevent 170. An apoptosis substrate aids in the prevention of apoptosis ofcells, and in particular cancer cells. The apoptosis substrate isselected from the group consisting of DMSO, Leptin, Glycine betaine,potassium citrate, Trimethylamine, proline, NDSB 195, L-Arginine,Xylitol, Sodium selenite, NDSB 201, CuCl₂, or CTAB.

The final concentration of the apoptosis substrate in the cell viabilityreagent is from about 0.001 M to about 0.5 M, or from about 0.1 mM, upto about 1 mM, up to about 10 mM, up to about 0.1 M, up to about 0.25 M,up to about 1 M, up to 1.5 M up to a maximum of about 2 M.

At event 180, the method of 100 further provides mixing the chaotrope,kosmotrope, chelator, buffer, apoptosis substrate, and the metabolicmodulator to enable the gene expression analysis of the tissue sample.The mixing of the samples may happen throughout the method offormulating the reagent of the invention. Each individual component istreated and mixed to obtain the optimal cell viability reagent. Theaddition of the components of the formulation maybe random; however, inmost embodiments the addition of the components is sequential in theorder shown in method 100.

The preparation time for producing the reagent varies due to the batchsize, temperature, etc. In general, it takes approximately one hour tocomplete the formulation of the cell viability reagent. The reagentmaybe stored at ambient conditions for up to 12 months prior to use ontissue samples. The reagent may also be frozen for longer storage.

Once a tissue sample has been added to the cell viability reagent, thetissue is stabilized and maintains viable gene expression components forup to 72 hours at 30° C. temperature. In general, the time the cells areviable is about 30 hours to about 50 hours and more particularly abouttwo days. This time frame is sufficient for detailed genetic expressionanalysis of tissues from biopsies (tissue samples) that can givesignificant insight into the types and progression of diseases such ascancer.

Referring to FIG. 2, there is a flow chart showing an embodiment of themethods for generating the cell viability reagent in accordance with theinvention. The method 200 comprises providing Sodium thiocyanate atevent 210. Sodium thiocyanate is a chaotrope and is added to purifiedwater and mixed thoroughly before adding the chelator EDTA at event 220.After the mixing of the EDTA into the solution, the metabolicmodulator/penetrant DMSO (Dimethylsulfoxide) is added to the mixture atevent 230.

At event 240 a first kosmotrope, glycerol, is added to the formulationof the reagent. The formulation is mixed until the solution is clear andthen the buffer component of the reagents is added in event 250. Thebuffer of the method showing in FIG. 2 is Sodium Phosphate Buffer(monobasic, tribasic PO₄). This buffer ensures that the pH of the finalcell viability reagent will be around about 7.0 to 7.6 and more likelyaround 7.2.

At event 260, a second kosmotrope, different from the first kosmotropeis added to the formulation. The second kosmotrope in method 200 isα,α-Trehalose.

At event 270, the method of 200 further comprises adding leptin and anapoptosis substrate which helps in the prevention of cellular apoptosis,particularly of cancerous cells.

At event 280, the method 200 further provides mixing of the componentsof the reagent formulation. After each component addition, mixing iscompleted to ensure the each component is solubilized within the reagentsolution.

TABLE I Viability/ Cell Viability study Trypan Blue Proliferation 1 day(24 hours) Cellular Clumps Viability MTT TAG-1 No Cell Clumps No DeadCells 100% TAG-2 Few Cell Clumps Many Dead Cells 53% Formalin CellDestroyed All Cells Dead 0%

Table I, above, shows the viability of Ishikawa cancer cells after oneday of being exposed to one embodiment of the preserving reagent withand without leptin added to the reagent, TAG-1 and TAG-2, respectively.TAG-1 and TAG-2, in Table 1 are compared to the viability of theIshikawa cancer cells when they are place in a 20% buffered formalinsolution. TAG-1 in Table I comprises Sodium Thiocyanate, EDTA, buffers,α,α-Trehalose, DMSO, Glycerol and Leptin. TAG-2 solution shown in Table1 comprises the same components of TAG-1 but without the presence ofLeptin.

Table 1 shows the viability of the cancer cells by measuring thepresence of cellular clumps in the solutions, trypan blue results forindication of the presence of dead cells and the viability/proliferationof the cells using MTT. The MTT assay is a colorimetric assay forassessing cell viability NAD(P)H-dependent cellular oxidoreductaseenzymes under defined conditions which reflects the number of viablecells present. These enzymes are capable of reducing the tetrazolium dyeto its insoluble formazan which has a purple color. Dead cells do notcause this color. The MTT dye is added to cell suspensions and read at aspectrophometric setting of 570 nm and a background wavelength 630/690nm. The density of viable cells and growing cells proliferation arecalculated using a ratio of dead cells (yellow color) to live cells(purple color) on a defined grid. The results shown in Table I indicatethat at 24 hours exposure to the preserving reagents, TAG-1 has 100%viability, TAG-2 has 53% viability and the formalin solution has 0%cellular viability.

TABLE II Viability/ Cell Viability study Trypan Blue Proliferation 8days (192 hours) Cellular Clumps Viability MTT TAG-1 Few Cell Clumps FewDead Cells 88.94% TAG-2 Diffuse Cell >95% Dead Cells    5% ClumpsFormalin Cell Destroyed All Cells Dead    0%

Table II, above, shows the viability of the Ishikawa cancer cells afterbeing exposed to TAG-1, TAG-2 or the formalin preserving solutions foreight days. The preserving reagents of the invention, TAG-1 and TAG-2,are the same as those used in the experiment shown in Table I. Aftereight days of exposure to the preserving reagents at room temperature,TAG-1 has a viability of 88.94%, TAG-2 has a cell viability of 5%, andin the formalin solution, all the cells were dead. These resultsindicate that the preserving reagent(s) of the invention is much betterat preserving cell viability over time than formalin. These results alsodemonstrate the importance of adding leptin as an apoptosis component.

When the reagent is prepared correctly it can act as a cancer tissuepreservative, maintaining cell viability in the tissue with a 95%viability for up to 24 hours. Viability from one to about five days canbe achieved with an average viability of about three days. The reagentalso aids in the inhibition or significant suppression of cancer cellapoptosis in tissue, controls cellular factors such as hypoxia, andhelps in the rapid inactivation of degrading enzymes to protect tissueand nucleic integrity.

Furthermore, approximately 90% tissue penetration is seen within twohours and the rapid buffering of the chemistry components to a pH of 7.2allows for maximum cellular metabolic activity of the reagentcomponents. The reagent of the invention allows for modulation ofcellular metabolic stress by biochemical mechanisms utilizingchaotropic, kosmotropic chemistries, buffering systems, and a novelcancer-stimulating hormone leptin which has been shown to increase thegrowth of cancer in obese patients. Adding a cryoprotectant such asglycerol which may act as a kosmotrope for protein preservation, mayalso impart thermo stability to the tissue specimen.

Another benefit of the reagent is that the reagent stabilizes geneexpression of target RNA and mRNA, measured by real time PCR ormicroarray methods. Rapid penetration of reagent components into cellsand tissue has been observed.

TABLE III RIN Formulation RIN control RIN RIN RIN 170 Chemistry 0 hours24 hours 72 hours 120 hours hours TAG-1 8.7 8.2 7.9 7.4 6.0 TAG-2 5.12.7 1.5 1.1 0 TAG-3 6.7 3.1 1.6 1.3 0 TAG-4 7.2 2.5 2.4 1.8 0 TAG-5 5.84.2 1.3 0 0

Table III show the results of a RNA integrity study comparing fivedifferent formulations of the cellular preserving reagent of theinvention. Ishikawa cancer cells were exposed or aged in the variousformulations for up to 170 hours prior to extracting RNA from the cells.The TAG-1 formulation comprises leptin and α,α-Trehalose, SodiumThiocyanate, EDTA, buffers, DMSO, and glycerol. TAG-2 formulation had noα,α-Trehalose or leptin present. TAG-3 formulation had no glycerol,leptin or α,α-Trehalose added. TAG-4 formulation had no DMSO, buffers orleptin. TAG-5 formulation had no Leptin, α,α-Trehalose, sodiumThiocyanate or EDTA.

The Ishikawa cancer cells utilized in the study shown in Table III areendometrial adenocarcinoma cells which were grown in DMEM media,supplemented with 5% bovine serum. The cells were seeded at a density of1×10⁶ on a 100 mm tissue culture dish. The cells were harvested usingtraditional methods and then resuspended in various formulations of thecell preserving reagent of the invention and left at room temperaturefor various amounts of time. At various time points the cellular RNA wasextracted using an RNeasy™ mini kit and the RNA was analyzed for qualityand quantity using the Agilent 2000 Bioanalyzer using the manufacturer'sstandard protocols. Controls for this study were archived purifiedcellular RNA.

The results shown on Table III indicate that the preferred embodiment ofthe invention comprises all of the elements shown in FIG. 2. The needfor α,α-Trehalose and Leptin in the cell preserving formulation of theinvention is clearly shown in Table III. The RNA Integrity Number (RIN)measured by the Agilent 2000 RNA analyzer has a scale from 1 to 10. Anynumber below 6 is considered to show degraded and unreliable RNA whichis not useful for gene expression studies. TAG-1 is the only formulationthat has a RIN number that stays above 6.0, even at the 170 hour timepoint. The final concentrations of the TAG-1 formulation embodiment ofthe invention was; Sodium Thiocyanate 0.01 M, EDTA 0.01 M, Glycerol 0.25M, Buffers 0.001 M, Leptin 0.001 M, α,α-Trehalose 0.20 M.

The reagent of the invention is also compatible with standard stainingpathology methods. Cells were treated in the TAG-1 reagent for 24 hoursand stained with Hematoxylin and Eosin stain using standard protocols.The stained cells were compared with untreated cells which were alsostained with hematoxylin Eosin stain using the same standard protocols.The cells were examined microscopically for cytoplasmic, nuclear, andextracellular matrix features. In both cell sets nuclei stained blue,whereas the cytoplasm and extracellular matrix had consistent pinkstaining. In summary there were no significant differences with stainingof TAG-1 treated cells and cells not treated with TAG-1 chemistry.

In most embodiments, the cell viability reagent comprises a chaotrope,at least one kosmotrope, a chelator, a buffer, a metabolic modulator,and an apoptosis substrate. These components of the reagent are found inlow molar concentrations compared to other tissue preservatives. Lowmolar concentrations of chaotropes act very differently and demonstratea very protective effect on the stability and preservation of nucleicacids, as well as having a major impact on cell metabolism by modifyingwater distribution and metabolism of cells as described herein. Basisfor U.S. Pat. No. 6,458,546 B1 (Baker). The final concentrations for thechaotrope is from about 0.1 M to about 2 M, the at least two kosmotropesare from about 0.1 M to about 2 M for each kosmotrope, the chelator isfrom about 0.1 M to about 2 M, and the apoptosis substrate is from about0.001 M to about 0.5 M. Unlike high molar concentrations of chaotropeswhich destroy cells and denature proteins and nucleic acids, lowerconcentration of the chaotropes have been shown to be beneficial inpreserving tissue samples. Also, low molar concentrations of kosmotropesare very synergistic with low concentrations of chaotropes in modifyingcellular metabolism, protecting proteins and nucleic acids. Optimumstabilization of biological macromolecules (e.g. cancer cells) requiresa mixture of one or more kosmotropic anions and a chaotropic action fromone of the following groups.

In certain embodiments, the chaotrope is SCN⁻ (sodium thiocyanate), thekosmotropes are glycerol and α,α-Trehalose, the chelator is EDTA, thebuffer is sodium phosphate buffer (monobasic, tribasic PO₄), the cellapoptosis substrate is leptin, and the metabolic modulator is DMSO.

The invention also provides kits for biopsy samples which comprise avessel, the vessel configured to hold a cell viability reagent, whereinthe cell viability reagent allows for genetic expression analyses of thebiopsy sample.

In most embodiments, the vessel in the kit is a cup or tube of amplesize to hold a biopsy tissue sample, as well as an aliquot of thereagent of the invention. The tube maybe an eppendorf tube or largerdepending on the size of the tissue sample to be analyzed. The reagentin the kit comprises at least one chaotrope, at least one kosmotrope, achelator, a buffer, an apoptosis substrate, and a metabolic modulator.

In other embodiments, the cup comprises a lid for sealing the cellviability reagent in the cup.

Preferred methods for manufacturing a cell viability reagent for tissuesamples, especially cancer tissue samples, are provided in the followingexamples.

EXAMPLES

The following preparations and example are given to enable those skilledin the art to more clearly understand and to practice the presentinvention. They should not be considered as limiting the scope of theinvention, but merely as being illustrative and representative thereof.

Example I

This example is a demonstration of one embodiment of the methods forproducing the reagent for maintaining cellular viability of a tissuesample. FIGS. 3A and 3B are pictures of a formulation sheet listing thecomponents of the reagent and instructions on how to prepare thecellular viability reagent for tissue biopsy samples. In this exampleone liter of reagent is made. The components on the formulation sheetare listed in the order they are to be added except for the purifiedwater which is measured out initially (50 mL). The chaotrope, 8.1 g ofsodium thiocyanate, is added to the water to give a final concentrationof sodium thiocyanate of 10% w/v. The sodium thiocyanate is mixed untilthe solution is clear. Following the addition of the chaotrope, EDTA,the chelator, is added to the solution at a stock concentration of 0.1M. 100 mL of 0.1 M EDTA is added to give a final concentration of 0.01 MEDTA in the reagent. The EDTA is mixed until the solution ishomogeneous. The next component added to the solution is the metabolicmodulator, DMSO. DMSO (20 mL) is added to the solution to give the finalpercentage of 2% DMSO in the reagent. After adding the DMSO, thesolution is mixed until it is homogeneous. The first kosmotrope,glycerol (25 mL) is then added to the solution giving the finalpercentage of glycerol in the reagent of 2.5%. The solution is mixedagain until homogeneous. The buffering components are then added to thesolution. KH₂PO₄ (3.93 g), monobasic potassium phosphate, is added firstand mixed to homogeneity, followed by the addition of 5.02 g of K₃PO₄,tribasic potassium phosphate. Once the solution is homogeneous, thesecond kosmotrope, α,α-Trehalose dihydrate is added to the solution.α,α-Trehalose dihydrate (7.56 g) is added to the reagent. The solutionis then mixed until clear. The final component added to the solution isthe apoptosis substrate, human leptin. 50 microliters (0.001 M) ofleptin is added to the solution which is then mixed until clear.

Purified water is then added to bring the volume up to one liter. All ofthe steps above are carried out a room temperature. The cellularviability reagent can be stored for up to one year under ambientconditions.

The formulation sheet of FIGS. 3A and 3B, as well as this example, is anexcellent representation of one embodiment of the methods in producingthe viable cell tissue reagent as well as a good example of thecomponents which comprise a viable cell tissue reagent in accordance ofthe invention.

Example II

Example II is a study of one embodiment of the tissue cell preservingreagent effectiveness on preserving LNCaP-FGC cells and PC-3 cells. Theresults for preserving LNCaP-FGC cells in TAG-1 reagent compared tostandard cell resuspension solutions are shown in FIG. 4. The resultsfor preserving PC-3 cells in TAG-1 reagent compared to standard cellresuspension solutions are shown in FIG. 5.

The Human Prostate cell lines DU145, PC-3 and LNCaP-FGC were purchasedfrom the American Type Collection (Manassas Va., USA). DU145 cells werecultured in DMEM media supplemented with 10% PBS plus Penicillin (100units/mL) and Streptomycin (100 μL/mL). PC-3 and LNCaP-FGC cells werecultured in RPMI 1640 media supplemented with 10% fetal bovine serum(FBS) and Penicillin (100 units/mL) and Streptomycin (100 μL/mL). Thecells were grown in tissue culture plates to a confluency of about 70%.The cells were then harvested by traditional methods and resuspended inone embodiment of the cell preserving reagent, TAG-1, or a controlsolution such as K₂EDTA, 20% Formalin, or Saline with Thimerosal.

The study using LNCaP-FGC cells compared the preservation effectivenessof TAG-1, a saline Thimerosal solution, and K₂EDTA solution. The cellswere resuspended in either TAG-1 or the control solutions and allowed toage for up to 100 hours. The TAG-1 solution was left at 25° C., whilethe K₂EDTA solution was kept at 4° C. At various time points, 0 hr, 24hr, 48 hr, 72 hr, and 100 hrs, the RNA was extracted from the aged cellsto determine the integrity of the mRNA from each sample. FIG. 4 is agraph showing the comparison of the cancer cells aged in the TAG-1reagent or the two control solutions. The copies of G6PDH mRNA weredetected for each time point using RT-PCR. FIG. 4 shows that the TAG-1solution kept the mRNA/cells viable better than the control solutions.The control solutions showed no copies of G6PDH at the 48 hr time pointor even earlier. The TAG-1 solution was able to still have viable cellswith intact mRNA even at 100 hours.

The study using PC-3 cells (FIG. 5) compared the preservationeffectiveness of TAG-1, a saline/thimerosal solution, and K₂EDTAsolution. The cells were resuspended in either TAG-1 or the controlsolutions and allowed to age for up to 100 hours. The TAG-1 solution wasleft at 25° C., while the K₂EDTA solution was kept at 4° C. At varioustime points, 0 hr, 24 hr, 48 hr, 72 hr, and 100 hrs, the RNA wasextracted from the aged cells to determine the integrity of the mRNAfrom each sample. FIG. 5 is a graph showing the comparison of the cancercells aged in the TAG-1 reagent or the two control solutions. The copiesof PBGD mRNA were detected for each time point using RT-PCR. FIG. 5shows that the TAG-1 solution kept the mRNA intact better than thecontrol solutions. The control solutions showed almost no copies of PBGDat the 48 hr time point. The TAG-1 solution was able to still haveviable cells with intact mRNA even at 100 hours.

The study using renal cancer cells compares one of the embodiments ofthe preserving reagent of the invention to two other solutions, onebeing 20% Formalin and the other being a K₂EDTA with Sodium Thiocyanatesolution. The renal cancer cells were grown and harvested in a similarmanner as the prostate cancer cell lines utilized above. The cells werethen aged for up to 100 hours in either TAG-1, 20% Formalin, or theK₂EDTA with Sodium Thiocyanate solution.

FIG. 6 shows a graph of the copies of G6PDH mRNA in the aged renalcancer cells detected by RT-PCR over time (0 hr, 24 hr, 48 hr, 72 hr and100 hr). The cells aged in the Formalin solution have no detectablecopies of G6PDH at 48 hours and the cells aged in K₂EDTA plus sodiumthiocyanate have no detectable mRNA G6PDH at 72 hours. The cells aged inthe TAG-1 formulation still have mRNA detectable at 100 hours.

The TAG-1 formulation for these experiments comprised Leptin,α,α-Trehalose, Sodium Thiocyanate, EDTA, buffers, DMSO and Glycerol.Final concentrations of the formulation were Sodium Thiocyanate 0.01 M,EDTA 0.01 M, Glycerol 0.25 M, Buffers 0.001 M, Leptin 0.001 M, andα,α-Trehalose 0.20 M.

Example III

Example III is a study showing the cell preservation effectiveness ofhaving α,α-Trehalose and Leptin in one of the embodiments of the tissuecell preserving reagent in accordance with the invention. Renal cancercells were used to compare the copies of G6PDH mRNA present over time (0hr, 24 hr, 48 hr, 72 hr, and 100 hr) for three formulations, TAG-1,TAG-1 without α,α-Trehalose, and TAG-1 without α,α-Trehalose and Leptin.The samples were left at room temperature before extracting the mRNAfrom the renal cells. FIG. 7 shows a graph of the comparison of thethree formulations of the number of copies of G6PDH mRNA is presentafter the renal cancer cells have been aged (resuspended in thepreserving solution) in one of the three cell preserving reagentsolutions. FIG. 7 clearly shows the effectiveness of having bothα,α-Trehalose and Leptin in the cell preserving formulation. TAG-1without α,α-Trehalose and TAG-1 without α,α-Trehalose and Leptin show nocopies of G6PDH mRNA at time point 48 hours, while mRNA G6PDH copies aredetected in the cells resuspended in the TAG-1 formulation even at the100 hour time point.

The TAG-1 formulation for these experiments comprised Leptin,α,α-Trehalose, Sodium Thiocyanate, EDTA, buffers, DMSO, and Glycerol.Final concentrations of the formulation were Sodium Thiocyanate 0.01 M,EDTA 0.01 M, Glycerol 0.25 M, Buffers 0.001 M, Leptin 0.001 M, andα,α-Trehalose 0.20 M.

Example IV

Example IV is a microarray study comparing gene expression patterns ofliquid nitrogen (LN₂) flash frozen tissue to tissue kept in oneembodiment of the invention, the TAG-1 cell preserving formulation. ThemRNA gene expression was completed on a Roche array 4-plex, 19K genes.The Array hybridization and scanning was performed through the Rocheinternal gene expression service using mRNA from Ishikawa cancer cellsprovided by Truckee Applied Genomics. The results were analyzed byextracting fluorescence from the array after alignment using quartilenormalization. Gene calls were generated using the Robust MultichipAverage (RMA) algorithm. Pairwise comparisons were visualized on scatterplots, and all treatments were compared by hierarchical clustering, bothstandard methods for array data visualization. Array quality control wasachieved by comparing expression distributions across 10 arrays with noapparent outliers.

Table IV below, shows the microarray experimental design. Tissue waseither aged in TAG-1 or stored for the specified time in LN₂.

TABLE IV 0 hr 24 hr 48 hr 72 hr 96 hr TAG-1 N = 1 N = 1 N = 1 N = 1 N =1 LN₂ N = 1 N = 1 N = 1 N = 1 N = 1

The pairwise correlation matrix is shown below in Table V in tabular andgraphical form. The experimental groups clustered with themselves, andin general showed good internal correlation.

TABLE V LN2 LN2 LN2 LN2 LN2 TAG TAG TAG 0 hr 24 hr 48 hr 72 hr 96 hr 0hr 24 hr 48 hr TAG 72 hr TAG 96 hr LN2 1 0.987 0.984 0.981 0.975 0.9710.94 0.922 0.873 0.89 0 hr LN2 0.987 1 0.99 0.991 0.982 0.974 0.9510.929 0.881 0.895 24 hr LN2 0.984 0.99 1 0.992 0.984 0.97 0.947 0.9250.876 0.891 48 hr LN2 0.981 0.991 0.992 1 0.986 0.966 0.946 0.926 0.8770.892 72 hr LN2 0.975 0.982 0.984 0.986 1 0.954 0.94 0.918 0.886 0.89796 hr TAG 0.971 0.974 0.97 0.966 0.954 1 0.96 0.934 0.871 0.885 0 hr TAG0.94 0.951 0.947 0.946 0.94 0.96 1 0.97 0.918 0.926 24 hr TAG 0.9220.929 0.925 0.926 0.918 0.934 0.97 1 0.951 0.965 48 hr TAG 0.873 0.8810.876 0.877 0.886 0.871 0.918 0.951 1 0.982 72 hr TAG 0.89 0.895 0.8910.892 0.897 0.885 0.926 0.965 0.982 1 96 hr

Regression Models:

For each of the 24,000 genes and each of the two experimental groups, alinear regression model was fit, with time as the independent variableand expression as the dependent variable. The model yielded a slope andan associated p-value for each gene. The slopes and p-values aresummarized in Table VI below.

TABLE VI Genes P < .05 Genes P < .01 Genes P < .001 TAG-1 5811 1696 197LN2 3101 786 85 Intersection 825 66 0 Genes P < .05 Genes P < .05 GenesP < .05 Slope > 0 Slope < 0 Total TAG-1 2597 3214 5811 LN2 1541 15603101 Absolute Slope, All Genes (Median, First to Third Quartile) TAG-1.13 (.09 to .23) LN2 .09 (.04 to .15) Units for slope = log2 expressionunits per day Absolute Slope, All Genes (Median, First to ThirdQuartile) TAG-1 7% (6% to 13.1%) LN2 6% (3% to 11%)   Units for slope =percent change per day

Variation Across Time:

For each of the 24,000 genes and each of the two experimental groups,the standard deviation and coefficient of variation across the five timepoints was computed, see TABLE VII below. These results were consistentwith the regression model results shown in TABLE VI above.

TABLE VII Gene Time Coefficient Gene Time Standard Deviation ofVariation Median Median (First to Third Quartile) (First to ThirdQuartile) TAG-1 0.484 (0.210 to 0.421) 32.8% (15.0% to 28.1%) LN2 0.277(0.199 to 0.376) 19.0% (13.7% to 25.7%)

Mean differences of the two sets are shown in TABLE VIII below. Overall,while there were significant mean difference between the groups, LN2 andTAG-1, the differences were well balanced between positive and negativedifferences.

Freezing tissues in liquid nitrogen is the gold standard for keepingcellular tissue intact. The above experiments compare the effectivenessof storing tissue in TAG-1 vs. liquid nitrogen. The above resultsindicate that the gene expression did not over or under express in cellsstored in TAG-1 compared to those stored in liquid nitrogen, indicatingthat TAG-1, over the time period tested was comparable to liquidnitrogen storage in preserving cellular integrity at the gene expressionlevel.

The TAG-1 formulation for these experiments comprised Leptin,α,α-Trehalose, Sodium Thiocyanate, EDTA, buffers, DMSO and Glycerol.Final concentrations of the formulation were Sodium Thiocyanate 0.01 M,EDTA 0.01 M, Glycerol 0.25 M, Buffers 0.001 M, Leptin 0.001 M, andα,α-Trehalose 0.20 M.

Example V

Example V is a study to evaluate media performance in ex vivo bladderand prostate cancer slice tissue cultures. Bladder and prostate tumortissues are stored for various lengths of time at room temperature inone embodiment of the invention, TAG-1. Slice viability over time isevaluated by examination of tissue morphology with standard microscopy,MTT assay for cell viability, TUNEL assay for apoptosis, and Ki67assessment of proliferation using immunostaining. Gene expression arrayexperiments will also be included in the assessment of the viability ofthe cancer tissues.

Comparisons will be made of slice cultures using a membrane system inwhich tissue slices (400-800 microns thick) will be maintained viaaccess to TAG-1 across a membrane covering a well. The optimizedprotocol with TAG-1 will be tested on chemotherapy drugs and clinicalsamples.

The general methodology comprises obtaining bladder and prostate cancertissue samples from NSG-PDX JAX mice or patient cancer biopsy cores.Tissue will be processed either as slices or as cut blocks, and culturedon culture plates in a 3D matrix or on a membrane. Normal tissue slicesfrom same patients will serve as controls to determine the differencesin behavior of cancer and normal tissue. In addition, isolatedperipheral blood mononuclear cells (PBMC) will be analyzed for theircorrelation to tumor cell behavior. Tissue samples are assayed atvarious time intervals for up to eight days in standardsaline/thimerosal solutions, K₂EDTA solution and TAG-1 for comparison ofTAG-1 to standard storage protocols.

The TAG-1 formulation for these experiments comprised Leptin,α,α-Trehalose, Sodium Thiocyanate, EDTA, buffers, DMSO, and Glycerol.Final concentrations of the formulation were Sodium Thiocyanate 0.01 M,EDTA 0.01 M, Glycerol 0.25 M, Buffers 0.001 M, Leptin 0.001 M, andα,α-Trehalose 0.20 M.

It is to be understood that the detailed description of illustrativeembodiments are provided for illustrative purposes. The scope of theclaims is not limited to these specific embodiments or examples.Therefore, various process limitations, elements, details, and uses candiffer from those just described, or be expanded on or implemented usingtechnologies not yet commercially viable, and yet still be within theinventive concepts of the present disclosure. The scope of the inventionis determined by the following claims and their legal equivalents.

1. A method of producing a cell viability reagent for a tissue sample,the method comprising: providing at least one chaotrope; providing afirst and a second kosmotrope, wherein the first kosmotrope is glyceroland the second kosmotrope is α,α-trealose; providing a chelator;providing a buffer; providing an apoptosis substrate, wherein theapoptosis substrate is leptin; providing a metabolic modulator; andmixing the at least one chaotrope, the first and second kosmotrope,chelator, buffer, apoptosis substrate, and the metabolic modulator toproduce the cell viability reagent, wherein the cell viability reagentis capable of preserving the tissue for gene expression analysis.
 2. Themethod of claim 1, wherein the tissue sample is a surgically excisedcancer tissue sample.
 3. (canceled)
 4. The method of claim 2, whereinthe chaotrope is selected from the group consisting of SCN (sodiumthiocyanate), H₂PO₄ ⁻, HCO₃ ⁻, I⁻, Cl⁻, NO₃ ⁻, NH₄ ⁻, NH₄ ⁺,guanidinium, and all salts of guanidinium.
 5. (canceled)
 6. The methodof claim 2, wherein chelator is selected from the group consisting ofEDTA, EGTA, and BAPTA.
 7. The method of claim 2, wherein the buffer isselected from the group consisting of BIS-TRIS, BIS-TRIS Propane, HEPES,MES, MOPS, and Sodium Phosphate Buffer.
 8. (canceled)
 9. The method ofclaim 2, wherein the metabolic modulator is selected from the groupconsisting of polar aprotic solvents, DMSO, Acetone,N,N-Dimethylformamide, and Acetonitrile.
 10. (canceled)
 11. The methodof claim 2, wherein the chaotrope is sodium thiocyanate, the firstkosmotrope is glycerol and a second kosmotrope is α,α-trehalose, thechelator is EDTA, the buffer is a Sodium Phosphate Buffer, the cellapoptosis substrate is leptin, and the metabolic modulator includes isDMSO.
 12. A method of manufacturing a cellular viability reagent foranalyzing a tissue sample, the method comprising: providing an aliquotof purified water; adding components of the reagent to the purifiedwater in the following order: adding sodium thiocyanate, followed by theaddition of EDTA, then adding DMSO, followed by adding glycerol, thenadding sodium phosphate, followed by the addition of α,α-trehalose,followed by adding leptin; and mixing the components between eachaddition of components in a manner that produces the cellular viabilityreagent, wherein the cellular viability reagent maintains the cellularRNA integrity of the tissue sample, which allows for accurate geneticexpression analysis of a tissue sample days after being placed in thereagent.
 13. (canceled)
 14. (canceled)
 15. A reagent for a tissue sampleto allow genetic expression analysis of a tissue sample, the reagentcomprising: at least one chaotrope; a first and a second kosmotrope; achelator; a buffer; an apoptosis substrate; and a metabolic modulator;wherein the chaotrope is selected from the group consisting of SCN(sodium thiocyanate), H₂PO₄ ⁻, HCO₃ ⁻, I⁻, Cl⁻, NO₃ ⁻, NH₄ ⁺, K⁺,guanidinium, and all salts of guanidinium, wherein the first kosmotropeis glycerol and the second kosmotrope is α,α-trehalose, wherein thechelator is selected from the group consisting of EDTA, EGTA, and BAPTA,wherein the buffer is selected from the group consisting of BIS-TRIS,BIS-TRIS Propane, HEPES, MES, MOPS, and Sodium Phosphate Buffer; whereinthe metabolic modulator is selected from the group consisting of polaraprotic solvents, DMSO, Acetone, N,N-Dimethylformamide and Acetonitrile;and wherein the apoptosis substrate is leptin.
 16. (canceled) 17.(canceled)
 18. The reagent of claim 15, wherein the chaotrope is SCN⁻(sodium thiocyanate), the at least one kosmotrope is a combination ofglycerol and α,α-trehalose, the chelator is EDTA, the buffer is SodiumPhosphate Buffer, the cell apoptosis substrate is leptin, and themetabolic modulator is DMSO. 19-30. (canceled)
 31. (canceled) 32.(canceled)
 33. (canceled)
 34. (canceled)
 35. (canceled)
 36. (canceled)37. (canceled)
 38. (canceled)
 39. (canceled)
 40. A method of preservinga biological sample by contacting the biological sample with a cellpreservation reagent comprising: a) a chelator; and b) leptin, whereinthe biological sample comprises a solid tumor.
 41. The method of claim40, further comprising: performing a gene expression analysis on thebiological sample.
 42. The method of claim 41, wherein the performingthe gene expression analysis comprises measuring quantities of RNAtranscribed from one or more genes in the biological sample.
 43. Themethod of claim 42, wherein quantities of RNA transcribed from one ormore genes in the biological sample are measured using PCR.
 44. Themethod of claim 42, wherein quantities of RNA transcribed from one ormore genes in the biological sample are measured using sequencing. 45.The method of claim 41, wherein the performing the gene expressionanalysis comprises measuring quantities of proteins in the biologicalsample.
 46. The method of claim 40, wherein a gene expression profile ofthe biological sample is substantially identical before and aftercontacting the biological sample with the cell preservation reagent. 47.The method of claim 40, wherein the biological sample is a surgicallyexcised cancer tissue sample.
 48. The method of claim 40, wherein thebiological sample is preserved for up to 72 hours after contacting thebiological sample with the cell preservation reagent.
 49. The method ofclaim 40, wherein preserving the biological sample comprises maintainingviable gene expression components within the biological sample.
 50. Themethod of claim 41, further comprising: generating a gene expressionprofile based on the gene expression analysis.
 51. The method of claim40, wherein the cell preservation reagent comprises a concentration ofleptin that is from about 0.001 M to about 2 M.
 52. The method of claim40, wherein the chelator is selected from the group consisting of EDTA,EGTA, and BAPTA.
 53. The method of claim 40, wherein the cellpreservation reagent further comprises a buffer that is selected fromthe group consisting of BIS-TRIS, BIS-TRIS Propane, HEPES, MES, MOPS,and Sodium Phosphate Buffer.